Main
Kasia Kedzierska
I am a 3rd year PhD student at the University of Oxford. I am a comuptational biologist, i.e. I use Data Science and Statistical Machine Learning while answering biological questions related to cancer of the uterus. Specifically, I study chromatin organisation in endometrial cancer. I spend most of my time either in command line writing Bash/Awk scripts or analysing and visualising data n R/Python.
I like teaching and deeply believe in Open Science. I am the President of #NGSchool Society with which I’ve been organising Summer Schoools in Bioinformatics. During last year edition - #NGSchool2019: Machine Learning for Biomedicine we recorded and published some of the lectures. This year, becasue of the pandemic we switched to organising virtual events, like NGSseminars series.
Research Experience
DPhil Candidate
Church group @ Wellcome Centre for Human Genetics, Wedge group @ Big Data Institute
University of Oxford, UK
2022 - 2018
- PhD project: Functional and evolutionary characterisation of chromatin organisation in endometrial cancer
Education
DPhil. Candidate, Genomic Medicine and Statistics
Nuffield Department of Medicine, Brasenose College
University of Oxford, UK
2022 - 2018
- Project: Functional and evolutionary characterisation of chromatin organisation in endometrial cancer.
- Wellcome Trust Studentship
M. Sc. Eng., Biotechnology
Warsaw University of Technology
Warsaw, Poland
2018 - 2015
- Thesis: Analysis of the mutational burden across gene sets in cancer.
- Thesis awarded the best Master thesis in Bioinformatics defended in 2018 title.
Publications
Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
Genome Research
N/A
2019
- Regulation networks in heart developmnent in zebrafish.
Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
BMC Cancer
N/A
2018
- DNA repair genes and androgen signalling in prostate cancer cell lines.
SONiCS: PCR stutter noise correction in genome-scale microsatellites
Bioinformatics
N/A
2018
- Tool for genotyping short tandem repeats (STRs) profiled using capture assays, github.com/kzkedzierska/sonics
Posters, and Talks
Analysis of the mutational burden across gene sets in cancer
Polish Bioinformatics Society Symposium
Cracow, Poland
2019
- Invited talk
Differential mutation analysis across gene sets in cancers
The Biology of Genomes 2018
Cold Spring Harbor, NY, USA
2018
- Poster
Awards and honours
Best Master Thesis in Bioinformatics
N/A
N/A
2019 - 2018
- The Best Master Thesis defended in the field of Bioinformatics in 2018 in Poland.
- Analysis of the mutational burden across gene sets in cancer Masther thesis defended at the Warsaw University of Technology; code for the analyses can be accessed github.com/kzkedzierska/cancers
Teaching Experience
Online tutorials: Python for Data Science and Introduction to Python
YouTube
2020
- I led two Python tutorials: Introduction to Python kasia.codes/talk/intro_to_python/ and Python for Data Science kasia.codes/talk/py4ds/.
Introduction to Managing Code with Git
Wellcome Centre for Human Genetics
Oxford, United Kingdom
2020 - 2019
- I led a 2-hour introduction to working with Git. Materials, including slides and exercises are available at kasia.codes/talk/into_to_git/.
Unsupervised learning, Introduction to Python
#NGSchool2019: Machine Learning for Biomedicine
Ostróda, Poland
2019
- Tutor for the Introduction to Python (3 h workshop) and for the Unsupervised learning (1,5 h lecture).
- Materials for the Introduction to Python are available on github
Introduction to R
Wellcome Centre for Human Genetics
Oxford, United Kingdom
2019
- 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
- Materials available on github/kzkedziersa/r_intro
Attended Workshops, Summer Schools
Machine Learning Summer School
Imperial College London, University College Londn
London, United Kingdom
2019
- 12-day intensive course on a variety of topics in machine learning.
Grants
Visegrad Grant to organize #NGSchool2020 - postponed until 2021
N/A
2021 - 2020
- 32,190 EUR awarded towards organising #NGSchool2020 and #NGSymposium. Both events are postponed until 2021.
Non profit work
President
N/A
2021 - 2018
- The goal of the Society is to promote and support science, with emphasis on computational biology.
- President since 2019; Vice President 2018 - 2019